Multiple sequence alignment - TraesCS6A01G418900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G418900 chr6A 100.000 8176 0 0 1 8176 616762510 616754335 0.000000e+00 15099
1 TraesCS6A01G418900 chr6A 91.477 176 10 1 1 171 359559298 359559473 3.810000e-58 237
2 TraesCS6A01G418900 chr6A 93.258 89 4 1 742 830 359560511 359560597 6.660000e-26 130
3 TraesCS6A01G418900 chr6A 93.258 89 4 1 742 830 489034140 489034226 6.660000e-26 130
4 TraesCS6A01G418900 chr6B 94.840 6512 238 43 1072 7523 718638623 718645096 0.000000e+00 10074
5 TraesCS6A01G418900 chr6B 94.128 596 13 8 6554 7149 669686670 669686097 0.000000e+00 887
6 TraesCS6A01G418900 chr6B 94.128 596 13 8 6554 7149 669740239 669739666 0.000000e+00 887
7 TraesCS6A01G418900 chr6B 89.391 443 27 7 645 1081 718638158 718638586 2.600000e-149 540
8 TraesCS6A01G418900 chr6B 91.644 371 19 7 7180 7549 669686096 669685737 3.410000e-138 503
9 TraesCS6A01G418900 chr6B 90.566 371 22 7 7180 7549 669739665 669739307 5.740000e-131 479
10 TraesCS6A01G418900 chr6B 93.603 297 12 4 7522 7816 718645210 718645501 3.500000e-118 436
11 TraesCS6A01G418900 chr6B 87.736 212 10 4 7969 8166 718645899 718646108 4.930000e-57 233
12 TraesCS6A01G418900 chr6B 90.476 168 8 4 7811 7974 718645692 718645855 1.790000e-51 215
13 TraesCS6A01G418900 chr6B 93.258 89 6 0 558 646 718638038 718638126 1.850000e-26 132
14 TraesCS6A01G418900 chr6D 95.366 2374 96 9 4270 6635 473233614 473235981 0.000000e+00 3762
15 TraesCS6A01G418900 chr6D 95.650 1678 62 8 2604 4274 473231906 473233579 0.000000e+00 2684
16 TraesCS6A01G418900 chr6D 95.717 1471 46 6 1072 2537 473230451 473231909 0.000000e+00 2351
17 TraesCS6A01G418900 chr6D 95.122 1189 45 5 6628 7816 473236005 473237180 0.000000e+00 1862
18 TraesCS6A01G418900 chr6D 91.096 438 21 6 645 1081 473229998 473230418 1.980000e-160 577
19 TraesCS6A01G418900 chr6D 85.359 362 27 17 7811 8163 473237366 473237710 1.310000e-92 351
20 TraesCS6A01G418900 chr6D 92.195 205 13 1 442 646 473229765 473229966 3.730000e-73 287
21 TraesCS6A01G418900 chr6D 88.108 185 6 6 195 370 473229588 473229765 1.080000e-48 206
22 TraesCS6A01G418900 chr5D 84.284 2278 211 74 5429 7655 398901188 398903369 0.000000e+00 2087
23 TraesCS6A01G418900 chr5D 85.304 1531 151 31 679 2194 398896543 398898014 0.000000e+00 1513
24 TraesCS6A01G418900 chr5D 90.144 1177 94 17 2655 3818 398898355 398899522 0.000000e+00 1511
25 TraesCS6A01G418900 chr5D 83.960 1091 121 25 4263 5342 398900092 398901139 0.000000e+00 996
26 TraesCS6A01G418900 chr5D 88.249 417 42 6 3815 4228 398899691 398900103 7.370000e-135 492
27 TraesCS6A01G418900 chr5D 83.938 193 18 8 2194 2378 398898059 398898246 1.090000e-38 172
28 TraesCS6A01G418900 chr5A 85.032 1570 153 39 644 2194 503941234 503942740 0.000000e+00 1522
29 TraesCS6A01G418900 chr5A 87.826 1150 87 22 5375 6513 503945796 503946903 0.000000e+00 1299
30 TraesCS6A01G418900 chr5A 90.526 950 63 14 2635 3575 503943107 503944038 0.000000e+00 1230
31 TraesCS6A01G418900 chr5A 84.517 1253 122 27 963 2194 109302746 109303947 0.000000e+00 1173
32 TraesCS6A01G418900 chr5A 84.688 1058 117 28 3815 4861 503944265 503945288 0.000000e+00 1014
33 TraesCS6A01G418900 chr5A 88.018 868 43 28 1 830 326895612 326896456 0.000000e+00 970
34 TraesCS6A01G418900 chr5A 86.902 878 43 24 1 830 285342505 285343358 0.000000e+00 918
35 TraesCS6A01G418900 chr5A 86.820 607 47 17 6814 7418 503947131 503947706 0.000000e+00 647
36 TraesCS6A01G418900 chr5A 85.545 505 54 9 4838 5342 503945305 503945790 2.040000e-140 510
37 TraesCS6A01G418900 chr5A 85.196 331 31 12 2209 2531 503942803 503943123 2.850000e-84 324
38 TraesCS6A01G418900 chr5A 90.299 134 10 3 2532 2664 482027337 482027206 1.090000e-38 172
39 TraesCS6A01G418900 chr5B 90.119 1174 96 15 2655 3818 479194691 479195854 0.000000e+00 1507
40 TraesCS6A01G418900 chr5B 84.307 1574 166 35 637 2194 479192811 479194319 0.000000e+00 1463
41 TraesCS6A01G418900 chr5B 87.462 1300 109 28 5429 6707 479197493 479198759 0.000000e+00 1448
42 TraesCS6A01G418900 chr5B 83.135 1091 120 26 4263 5342 479196407 479197444 0.000000e+00 937
43 TraesCS6A01G418900 chr5B 82.319 854 101 29 6814 7655 479198851 479199666 0.000000e+00 695
44 TraesCS6A01G418900 chr5B 87.740 416 29 12 3815 4228 479196023 479196418 4.470000e-127 466
45 TraesCS6A01G418900 chr5B 84.348 345 29 11 2194 2531 479194364 479194690 1.710000e-81 315
46 TraesCS6A01G418900 chr5B 90.071 141 11 3 2532 2671 413609487 413609625 6.520000e-41 180
47 TraesCS6A01G418900 chr1B 84.278 1253 125 26 963 2194 674639818 674638617 0.000000e+00 1157
48 TraesCS6A01G418900 chr1B 81.755 433 42 20 728 1156 545451734 545452133 2.200000e-85 327
49 TraesCS6A01G418900 chr2B 83.879 1253 130 27 963 2194 10670138 10671339 0.000000e+00 1129
50 TraesCS6A01G418900 chr2B 83.320 1253 130 28 963 2194 390973496 390972302 0.000000e+00 1083
51 TraesCS6A01G418900 chr2B 78.846 520 68 20 644 1158 736737698 736737216 6.160000e-81 313
52 TraesCS6A01G418900 chr2A 83.799 1253 131 26 963 2194 130176988 130175787 0.000000e+00 1123
53 TraesCS6A01G418900 chr2A 86.598 873 47 22 1 830 480822611 480821766 0.000000e+00 900
54 TraesCS6A01G418900 chr2A 79.423 520 64 23 644 1156 537056950 537057433 2.200000e-85 327
55 TraesCS6A01G418900 chr2A 93.182 176 7 1 1 171 34216186 34216361 3.790000e-63 254
56 TraesCS6A01G418900 chr2A 87.273 110 4 5 265 370 537056570 537056673 5.180000e-22 117
57 TraesCS6A01G418900 chr1A 87.414 874 39 24 1 830 52663923 52664769 0.000000e+00 939
58 TraesCS6A01G418900 chr1A 92.614 176 8 2 1 171 378549350 378549175 1.760000e-61 248
59 TraesCS6A01G418900 chr4A 86.727 889 35 29 1 830 520591455 520592319 0.000000e+00 911
60 TraesCS6A01G418900 chr4A 78.958 518 66 23 644 1156 696445401 696445880 6.160000e-81 313
61 TraesCS6A01G418900 chr7B 80.695 518 59 21 644 1156 697783958 697783477 1.680000e-96 364
62 TraesCS6A01G418900 chr7B 84.483 116 8 4 265 376 697784338 697784229 1.120000e-18 106
63 TraesCS6A01G418900 chr7A 96.364 165 6 0 1 165 38181361 38181525 1.050000e-68 272
64 TraesCS6A01G418900 chr7A 93.182 176 7 1 1 171 569589003 569588828 3.790000e-63 254
65 TraesCS6A01G418900 chr7A 92.899 169 8 3 1 165 609952072 609951904 8.200000e-60 243
66 TraesCS6A01G418900 chr7A 91.538 130 9 2 2532 2661 731392033 731392160 2.340000e-40 178
67 TraesCS6A01G418900 chr7A 94.382 89 3 1 742 830 569579032 569578946 1.430000e-27 135
68 TraesCS6A01G418900 chr3A 94.220 173 8 2 1 171 561784218 561784390 6.290000e-66 263
69 TraesCS6A01G418900 chr3A 94.152 171 10 0 1 171 126387476 126387306 2.260000e-65 261
70 TraesCS6A01G418900 chr3A 91.908 173 12 1 1 171 698548046 698547874 2.950000e-59 241
71 TraesCS6A01G418900 chr4D 92.857 126 8 1 2532 2657 245650730 245650854 1.810000e-41 182
72 TraesCS6A01G418900 chr3D 91.538 130 10 1 2532 2661 182097555 182097683 2.340000e-40 178
73 TraesCS6A01G418900 chr3B 90.226 133 11 2 2532 2664 703007089 703006959 1.090000e-38 172
74 TraesCS6A01G418900 chrUn 88.971 136 11 3 2532 2664 451362413 451362279 1.830000e-36 165
75 TraesCS6A01G418900 chr4B 89.474 133 10 3 2532 2661 320 451 1.830000e-36 165


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G418900 chr6A 616754335 616762510 8175 True 15099.000000 15099 100.000000 1 8176 1 chr6A.!!$R1 8175
1 TraesCS6A01G418900 chr6B 718638038 718646108 8070 False 1938.333333 10074 91.550667 558 8166 6 chr6B.!!$F1 7608
2 TraesCS6A01G418900 chr6B 669685737 669686670 933 True 695.000000 887 92.886000 6554 7549 2 chr6B.!!$R1 995
3 TraesCS6A01G418900 chr6B 669739307 669740239 932 True 683.000000 887 92.347000 6554 7549 2 chr6B.!!$R2 995
4 TraesCS6A01G418900 chr6D 473229588 473237710 8122 False 1510.000000 3762 92.326625 195 8163 8 chr6D.!!$F1 7968
5 TraesCS6A01G418900 chr5D 398896543 398903369 6826 False 1128.500000 2087 85.979833 679 7655 6 chr5D.!!$F1 6976
6 TraesCS6A01G418900 chr5A 109302746 109303947 1201 False 1173.000000 1173 84.517000 963 2194 1 chr5A.!!$F1 1231
7 TraesCS6A01G418900 chr5A 326895612 326896456 844 False 970.000000 970 88.018000 1 830 1 chr5A.!!$F3 829
8 TraesCS6A01G418900 chr5A 503941234 503947706 6472 False 935.142857 1522 86.519000 644 7418 7 chr5A.!!$F4 6774
9 TraesCS6A01G418900 chr5A 285342505 285343358 853 False 918.000000 918 86.902000 1 830 1 chr5A.!!$F2 829
10 TraesCS6A01G418900 chr5B 479192811 479199666 6855 False 975.857143 1507 85.632857 637 7655 7 chr5B.!!$F2 7018
11 TraesCS6A01G418900 chr1B 674638617 674639818 1201 True 1157.000000 1157 84.278000 963 2194 1 chr1B.!!$R1 1231
12 TraesCS6A01G418900 chr2B 10670138 10671339 1201 False 1129.000000 1129 83.879000 963 2194 1 chr2B.!!$F1 1231
13 TraesCS6A01G418900 chr2B 390972302 390973496 1194 True 1083.000000 1083 83.320000 963 2194 1 chr2B.!!$R1 1231
14 TraesCS6A01G418900 chr2A 130175787 130176988 1201 True 1123.000000 1123 83.799000 963 2194 1 chr2A.!!$R1 1231
15 TraesCS6A01G418900 chr2A 480821766 480822611 845 True 900.000000 900 86.598000 1 830 1 chr2A.!!$R2 829
16 TraesCS6A01G418900 chr2A 537056570 537057433 863 False 222.000000 327 83.348000 265 1156 2 chr2A.!!$F2 891
17 TraesCS6A01G418900 chr1A 52663923 52664769 846 False 939.000000 939 87.414000 1 830 1 chr1A.!!$F1 829
18 TraesCS6A01G418900 chr4A 520591455 520592319 864 False 911.000000 911 86.727000 1 830 1 chr4A.!!$F1 829
19 TraesCS6A01G418900 chr7B 697783477 697784338 861 True 235.000000 364 82.589000 265 1156 2 chr7B.!!$R1 891

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
37 38 0.396060 CCTCCCTTCCATCTGCTAGC 59.604 60.000 8.10 8.10 0.00 3.42 F
1308 1539 0.727398 GCTCGGTTAGTGCATTGACC 59.273 55.000 12.58 12.58 39.04 4.02 F
1543 1776 0.744771 GTCTCAGGTTCGAATGCCCC 60.745 60.000 0.00 0.00 0.00 5.80 F
1809 2054 1.185315 GTGGAATGAACATGGGTGGG 58.815 55.000 0.00 0.00 0.00 4.61 F
3431 3778 1.215173 TGCCTGTTATTATGCAGCCCT 59.785 47.619 0.00 0.00 0.00 5.19 F
3888 4414 1.173913 GCCACCTAGGAAAAATGCGT 58.826 50.000 17.98 0.00 41.22 5.24 F
4168 4713 3.007940 TGGTTATAGATGGAAGGGCATCG 59.992 47.826 0.00 0.00 33.37 3.84 F
5167 5803 2.330286 TGTTATGAACACGTACGCAGG 58.670 47.619 16.72 7.94 36.25 4.85 F
6003 6640 0.527113 TGATGCAGCCGGTTCATTTG 59.473 50.000 1.90 0.00 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 2069 0.467290 TGGTGCCCAAGTTTGAGGAC 60.467 55.000 0.00 0.00 0.00 3.85 R
3180 3524 0.608640 ACTCCTTGCTTCCGTAGTGG 59.391 55.000 0.00 0.00 40.09 4.00 R
3431 3778 6.436218 TGAGGTTCAATAAGTACAGAGTAGCA 59.564 38.462 0.00 0.00 0.00 3.49 R
3770 4122 1.588082 GTCAGCTGCATGGGGTTTG 59.412 57.895 9.47 0.00 0.00 2.93 R
4568 5151 1.133976 GTATGGCTGTCTTGATGCCCT 60.134 52.381 12.47 7.48 45.56 5.19 R
5167 5803 2.052782 AACCCAACTGACCTTGACAC 57.947 50.000 0.00 0.00 0.00 3.67 R
5519 6156 2.477825 CAGTTGCTCGTATGATCCCAG 58.522 52.381 0.00 0.00 0.00 4.45 R
7025 7724 1.335964 GCGCGTAGAGATGCTGGATAA 60.336 52.381 8.43 0.00 35.24 1.75 R
7598 8428 0.031178 CAAGCACAACAGTTGCTCCC 59.969 55.000 13.56 0.00 38.01 4.30 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.305009 CAATTCCTCCCTTCCATCTGC 58.695 52.381 0.00 0.00 0.00 4.26
37 38 0.396060 CCTCCCTTCCATCTGCTAGC 59.604 60.000 8.10 8.10 0.00 3.42
38 39 1.422531 CTCCCTTCCATCTGCTAGCT 58.577 55.000 17.23 0.00 0.00 3.32
39 40 2.603021 CTCCCTTCCATCTGCTAGCTA 58.397 52.381 17.23 4.41 0.00 3.32
40 41 2.562298 CTCCCTTCCATCTGCTAGCTAG 59.438 54.545 16.84 16.84 0.00 3.42
41 42 1.622811 CCCTTCCATCTGCTAGCTAGG 59.377 57.143 22.10 12.03 0.00 3.02
42 43 2.324541 CCTTCCATCTGCTAGCTAGGT 58.675 52.381 22.10 5.20 0.00 3.08
56 63 2.369532 AGCTAGGTCTAGGTCTAGGTCG 59.630 54.545 14.75 0.00 39.45 4.79
107 129 2.041216 AGTGGTGAAGGAAATGGGGTAC 59.959 50.000 0.00 0.00 0.00 3.34
167 189 8.854117 AGGGATTGTTTATTAGATGCAAATCTC 58.146 33.333 0.00 0.00 32.36 2.75
173 203 7.011389 TGTTTATTAGATGCAAATCTCTCACCG 59.989 37.037 0.00 0.00 32.36 4.94
201 231 2.692041 CTGAATTCCCTTCCTTCATGGC 59.308 50.000 2.27 0.00 35.26 4.40
376 447 3.326588 TGTATAAGCAACACCTCACCTGT 59.673 43.478 0.00 0.00 0.00 4.00
377 448 3.508845 ATAAGCAACACCTCACCTGTT 57.491 42.857 0.00 0.00 31.80 3.16
378 449 2.143876 AAGCAACACCTCACCTGTTT 57.856 45.000 0.00 0.00 29.02 2.83
379 450 1.392589 AGCAACACCTCACCTGTTTG 58.607 50.000 0.00 0.00 29.02 2.93
380 451 1.102978 GCAACACCTCACCTGTTTGT 58.897 50.000 0.00 0.00 29.02 2.83
381 452 2.092646 AGCAACACCTCACCTGTTTGTA 60.093 45.455 0.00 0.00 29.02 2.41
382 453 2.884639 GCAACACCTCACCTGTTTGTAT 59.115 45.455 0.00 0.00 29.02 2.29
384 455 4.517453 GCAACACCTCACCTGTTTGTATAA 59.483 41.667 0.00 0.00 29.02 0.98
386 457 4.324267 ACACCTCACCTGTTTGTATAAGC 58.676 43.478 0.00 0.00 0.00 3.09
387 458 4.202419 ACACCTCACCTGTTTGTATAAGCA 60.202 41.667 0.00 0.00 0.00 3.91
388 459 4.393062 CACCTCACCTGTTTGTATAAGCAG 59.607 45.833 8.78 8.78 42.66 4.24
395 466 3.941483 CTGTTTGTATAAGCAGGACCAGG 59.059 47.826 7.99 0.00 40.28 4.45
396 467 3.585289 TGTTTGTATAAGCAGGACCAGGA 59.415 43.478 0.00 0.00 0.00 3.86
397 468 3.906720 TTGTATAAGCAGGACCAGGAC 57.093 47.619 0.00 0.00 0.00 3.85
398 469 2.116238 TGTATAAGCAGGACCAGGACC 58.884 52.381 0.00 0.00 0.00 4.46
399 470 2.116238 GTATAAGCAGGACCAGGACCA 58.884 52.381 10.90 0.00 0.00 4.02
400 471 1.207791 ATAAGCAGGACCAGGACCAG 58.792 55.000 10.90 3.18 0.00 4.00
401 472 0.909610 TAAGCAGGACCAGGACCAGG 60.910 60.000 10.90 0.33 0.00 4.45
402 473 3.721706 GCAGGACCAGGACCAGGG 61.722 72.222 10.90 4.22 0.00 4.45
403 474 3.721706 CAGGACCAGGACCAGGGC 61.722 72.222 10.90 3.59 0.00 5.19
404 475 4.270153 AGGACCAGGACCAGGGCA 62.270 66.667 11.56 0.00 35.15 5.36
405 476 3.721706 GGACCAGGACCAGGGCAG 61.722 72.222 11.56 0.00 35.15 4.85
416 487 1.617947 CCAGGGCAGGTCTGTCTACC 61.618 65.000 2.48 0.00 40.06 3.18
418 489 0.905337 AGGGCAGGTCTGTCTACCAC 60.905 60.000 2.48 0.00 42.40 4.16
476 590 2.558359 CAGGCCGGTGATTTTCTTTCTT 59.442 45.455 1.90 0.00 0.00 2.52
477 591 3.005791 CAGGCCGGTGATTTTCTTTCTTT 59.994 43.478 1.90 0.00 0.00 2.52
478 592 3.255888 AGGCCGGTGATTTTCTTTCTTTC 59.744 43.478 1.90 0.00 0.00 2.62
479 593 3.255888 GGCCGGTGATTTTCTTTCTTTCT 59.744 43.478 1.90 0.00 0.00 2.52
584 698 0.819259 ACGCTGTTTGCAGTCACCAT 60.819 50.000 0.00 0.00 44.32 3.55
636 750 4.341520 ACTCGGTCCTGGATACTTATTCAC 59.658 45.833 0.00 0.00 37.61 3.18
699 861 6.198591 GCTAAAGTTCAGATATGTACGTGTCC 59.801 42.308 8.10 0.00 0.00 4.02
700 862 5.916661 AAGTTCAGATATGTACGTGTCCT 57.083 39.130 8.10 0.00 0.00 3.85
701 863 5.250235 AGTTCAGATATGTACGTGTCCTG 57.750 43.478 8.10 7.34 0.00 3.86
702 864 4.705507 AGTTCAGATATGTACGTGTCCTGT 59.294 41.667 8.10 0.00 0.00 4.00
703 865 4.895224 TCAGATATGTACGTGTCCTGTC 57.105 45.455 8.10 0.00 0.00 3.51
704 866 3.630769 TCAGATATGTACGTGTCCTGTCC 59.369 47.826 8.10 0.00 0.00 4.02
789 960 4.385146 GTCCTGACTAGCTCGTTTGTTTAC 59.615 45.833 0.00 0.00 0.00 2.01
902 1079 9.959721 ATTTACAAGTAACTAATGGATGTGTCT 57.040 29.630 0.00 0.00 0.00 3.41
924 1102 1.896220 TTCTGTTTCAGATTGCGGCT 58.104 45.000 0.00 0.00 40.39 5.52
1014 1192 1.741770 AACGATGTCCGGCTTGCTC 60.742 57.895 0.00 0.00 43.93 4.26
1032 1210 4.842574 TGCTCAATGTACTTGCTTATCCA 58.157 39.130 0.00 0.00 34.66 3.41
1033 1211 5.252547 TGCTCAATGTACTTGCTTATCCAA 58.747 37.500 0.00 0.00 34.66 3.53
1034 1212 5.887598 TGCTCAATGTACTTGCTTATCCAAT 59.112 36.000 0.00 0.00 34.66 3.16
1035 1213 6.377996 TGCTCAATGTACTTGCTTATCCAATT 59.622 34.615 0.00 0.00 34.66 2.32
1036 1214 6.914757 GCTCAATGTACTTGCTTATCCAATTC 59.085 38.462 0.00 0.00 34.66 2.17
1037 1215 7.415541 GCTCAATGTACTTGCTTATCCAATTCA 60.416 37.037 0.00 0.00 34.66 2.57
1038 1216 8.347004 TCAATGTACTTGCTTATCCAATTCAA 57.653 30.769 0.00 0.00 34.66 2.69
1039 1217 8.801299 TCAATGTACTTGCTTATCCAATTCAAA 58.199 29.630 0.00 0.00 34.66 2.69
1040 1218 9.590451 CAATGTACTTGCTTATCCAATTCAAAT 57.410 29.630 0.00 0.00 0.00 2.32
1041 1219 9.807649 AATGTACTTGCTTATCCAATTCAAATC 57.192 29.630 0.00 0.00 0.00 2.17
1073 1251 4.372656 GAGGACTACCATGCATTCACTAC 58.627 47.826 0.00 0.00 38.94 2.73
1129 1353 9.841295 ACTAGGTTTTGTTATTACTTGTCTTGA 57.159 29.630 0.00 0.00 0.00 3.02
1152 1376 6.319658 TGATGATAACTTGATGCTTTCTTCCC 59.680 38.462 0.00 0.00 0.00 3.97
1173 1397 4.321230 CCCTTGGCAGTCAAATCTTAACAC 60.321 45.833 0.00 0.00 34.56 3.32
1308 1539 0.727398 GCTCGGTTAGTGCATTGACC 59.273 55.000 12.58 12.58 39.04 4.02
1323 1554 1.521681 GACCTAGTGCGCCATCCAC 60.522 63.158 4.18 0.00 0.00 4.02
1543 1776 0.744771 GTCTCAGGTTCGAATGCCCC 60.745 60.000 0.00 0.00 0.00 5.80
1574 1809 5.979517 GTGGAGGTTTGCAGCATTATTATTC 59.020 40.000 0.00 0.00 0.00 1.75
1809 2054 1.185315 GTGGAATGAACATGGGTGGG 58.815 55.000 0.00 0.00 0.00 4.61
1824 2069 1.618343 GGTGGGACCATTCAAGGTTTG 59.382 52.381 0.00 0.00 43.38 2.93
2357 2674 7.867909 GTGATGCTATAGTGTATTGCAGACTTA 59.132 37.037 0.84 0.00 46.70 2.24
2440 2759 9.929180 GGAGCCAACTTTTAGAATTTAGAATTT 57.071 29.630 0.00 0.00 0.00 1.82
2512 2839 3.440173 TCGCTATTCTTTCTTTTGCAGGG 59.560 43.478 0.00 0.00 0.00 4.45
2817 3150 6.962182 AGTCTCATGAGGGTGAATGATAAAA 58.038 36.000 22.42 0.00 32.56 1.52
2854 3187 7.110511 GTGTTATTTTCTTTTGTTGAACTGCG 58.889 34.615 0.00 0.00 0.00 5.18
3180 3524 4.036144 GCCAATCTCTCTTAATTGCAGGAC 59.964 45.833 0.00 0.00 32.65 3.85
3288 3632 4.525100 TGCCAGGATTTAAAGGTTGTTACC 59.475 41.667 0.00 0.00 45.39 2.85
3424 3771 6.441093 AATATCGGCATGCCTGTTATTATG 57.559 37.500 33.07 15.06 0.00 1.90
3431 3778 1.215173 TGCCTGTTATTATGCAGCCCT 59.785 47.619 0.00 0.00 0.00 5.19
3709 4060 5.480642 TGGCACACCATTTTTGTGAATAT 57.519 34.783 6.66 0.00 46.18 1.28
3888 4414 1.173913 GCCACCTAGGAAAAATGCGT 58.826 50.000 17.98 0.00 41.22 5.24
4168 4713 3.007940 TGGTTATAGATGGAAGGGCATCG 59.992 47.826 0.00 0.00 33.37 3.84
4198 4743 3.024547 TCGTGTTTTCCATTGGTCCAAA 58.975 40.909 8.75 0.00 0.00 3.28
4233 4778 8.465273 AAAACATGAGCTAAATATTACTCCCC 57.535 34.615 0.00 0.00 0.00 4.81
4249 4794 3.260205 CTCCCCCTGTCCCACAATATAT 58.740 50.000 0.00 0.00 0.00 0.86
4253 4798 3.394274 CCCCTGTCCCACAATATATGACA 59.606 47.826 3.59 3.59 34.95 3.58
4398 4981 8.147058 CAGTAAGTTAACTATGAGCCTCATGAT 58.853 37.037 17.46 5.80 37.70 2.45
4431 5014 4.321899 CGTGGACCAATGTGGATCAAAATT 60.322 41.667 0.00 0.00 40.96 1.82
4559 5142 8.988934 GTGTCTCAGACAATTTGTATTCTTGTA 58.011 33.333 9.73 0.00 44.49 2.41
4568 5151 3.965379 TGTATTCTTGTACCCGCTTCA 57.035 42.857 0.00 0.00 0.00 3.02
4616 5199 5.049060 TGAATACAAATAGTTGCACTTGCGT 60.049 36.000 2.17 0.00 45.83 5.24
4755 5343 6.214615 TCTGGTGTCATTCTCCTTTAATGGTA 59.785 38.462 7.24 0.00 35.48 3.25
4785 5374 7.147976 GTGTTCTGCATGGTTTTAATCTTTCT 58.852 34.615 0.00 0.00 0.00 2.52
4872 5501 7.908601 CACGGAATAAAATAAGACCTTTGTAGC 59.091 37.037 0.00 0.00 0.00 3.58
4888 5517 5.376854 TTGTAGCATTTCTTGAGGCTTTC 57.623 39.130 0.00 0.00 37.79 2.62
5077 5713 3.073678 TGTACCTGTAATGCAAGCACAG 58.926 45.455 15.24 15.24 39.50 3.66
5167 5803 2.330286 TGTTATGAACACGTACGCAGG 58.670 47.619 16.72 7.94 36.25 4.85
5512 6149 4.991687 CCACTAAACTCTCAGAGTCAAACC 59.008 45.833 8.09 0.00 42.59 3.27
5519 6156 5.007682 ACTCTCAGAGTCAAACCTCTAGTC 58.992 45.833 0.00 0.00 38.71 2.59
5752 6389 5.047377 TGCTTTGGGAATAGATTTGACAACC 60.047 40.000 0.00 0.00 0.00 3.77
5914 6551 3.606687 CTCCCGCCAATTACTACTGTTT 58.393 45.455 0.00 0.00 0.00 2.83
6003 6640 0.527113 TGATGCAGCCGGTTCATTTG 59.473 50.000 1.90 0.00 0.00 2.32
6385 7025 2.706190 AGGGAACATACTGCTATGTCCC 59.294 50.000 17.09 17.09 41.92 4.46
6392 7032 4.284490 ACATACTGCTATGTCCCGATCAAT 59.716 41.667 0.00 0.00 39.02 2.57
6394 7034 4.156455 ACTGCTATGTCCCGATCAATTT 57.844 40.909 0.00 0.00 0.00 1.82
6396 7036 4.576463 ACTGCTATGTCCCGATCAATTTTC 59.424 41.667 0.00 0.00 0.00 2.29
6410 7050 9.956720 CCGATCAATTTTCTAATGCTAAAGAAT 57.043 29.630 0.00 0.00 32.05 2.40
6460 7110 5.280164 GCCCATTGACTGTCATGGATCTATA 60.280 44.000 26.73 7.80 36.31 1.31
6557 7207 5.537300 TTCATGATCCACTTAGCTACCTC 57.463 43.478 0.00 0.00 0.00 3.85
6804 7487 1.875009 TCACAACTGAGCAGAGCTTG 58.125 50.000 4.21 1.53 39.88 4.01
6910 7609 3.823873 ACGGCAATGGTTCACAAGAATTA 59.176 39.130 0.00 0.00 35.92 1.40
7025 7724 1.210234 TGCATCCGTCTGGTGAATGAT 59.790 47.619 0.00 0.00 36.30 2.45
7066 7765 3.061563 GCACACTTGTTGCATTGCATATG 59.938 43.478 12.95 9.43 38.76 1.78
7067 7766 4.487019 CACACTTGTTGCATTGCATATGA 58.513 39.130 12.95 0.00 38.76 2.15
7068 7767 5.106442 CACACTTGTTGCATTGCATATGAT 58.894 37.500 12.95 0.00 38.76 2.45
7090 7789 4.640364 TGATAGTTGAGCATGTGTGTTGA 58.360 39.130 0.00 0.00 0.00 3.18
7156 7855 2.593956 GGCCAAGTCTCCCTTCCGT 61.594 63.158 0.00 0.00 0.00 4.69
7400 8103 5.964758 AGATACTCTCTTCTGCAGTGAAAG 58.035 41.667 14.67 10.39 0.00 2.62
7434 8137 0.030638 CGGTTGAACAGCACTTTGGG 59.969 55.000 0.00 0.00 0.00 4.12
7443 8146 6.686630 TGAACAGCACTTTGGGTTATTTATG 58.313 36.000 0.00 0.00 0.00 1.90
7447 8150 6.377146 ACAGCACTTTGGGTTATTTATGTAGG 59.623 38.462 0.00 0.00 0.00 3.18
7448 8151 5.359860 AGCACTTTGGGTTATTTATGTAGGC 59.640 40.000 0.00 0.00 0.00 3.93
7450 8153 6.350612 GCACTTTGGGTTATTTATGTAGGCAA 60.351 38.462 0.00 0.00 0.00 4.52
7451 8154 7.033185 CACTTTGGGTTATTTATGTAGGCAAC 58.967 38.462 0.00 0.00 0.00 4.17
7512 8217 7.865706 TTGTAGGAAAGAAAATGCCTCTATC 57.134 36.000 0.00 0.00 32.04 2.08
7598 8428 1.297664 GACTCATGCTGCTAGCCAAG 58.702 55.000 13.29 4.84 41.51 3.61
7599 8429 0.107312 ACTCATGCTGCTAGCCAAGG 60.107 55.000 13.29 0.00 41.51 3.61
7609 8439 0.326264 CTAGCCAAGGGAGCAACTGT 59.674 55.000 0.00 0.00 0.00 3.55
7675 8506 1.482593 AGCGGTAATCCACTTCTGAGG 59.517 52.381 0.00 0.00 0.00 3.86
7695 8526 2.851102 AGGGTCAGCTGCACCTGT 60.851 61.111 23.11 13.56 33.96 4.00
7703 8534 2.047844 CTGCACCTGTCCTGACGG 60.048 66.667 0.00 0.00 37.44 4.79
7755 8586 3.380004 TCAAGCCGCTTTCTTTTGAGAAA 59.620 39.130 1.86 2.08 36.49 2.52
7756 8587 4.111916 CAAGCCGCTTTCTTTTGAGAAAA 58.888 39.130 1.86 0.00 37.35 2.29
7757 8588 4.385358 AGCCGCTTTCTTTTGAGAAAAA 57.615 36.364 3.52 0.00 37.35 1.94
7758 8589 4.363138 AGCCGCTTTCTTTTGAGAAAAAG 58.637 39.130 4.87 4.87 40.25 2.27
7851 8900 7.701924 CGTTGGGAAAGATAGTATGTTAACGTA 59.298 37.037 13.56 3.32 33.53 3.57
7909 8958 2.497273 GGTCCCTGTTGCTTTTATGCAT 59.503 45.455 3.79 3.79 42.96 3.96
7910 8959 3.514645 GTCCCTGTTGCTTTTATGCATG 58.485 45.455 10.16 0.00 42.96 4.06
7911 8960 2.094078 TCCCTGTTGCTTTTATGCATGC 60.094 45.455 11.82 11.82 42.96 4.06
7912 8961 2.353903 CCCTGTTGCTTTTATGCATGCA 60.354 45.455 25.04 25.04 42.96 3.96
7913 8962 2.669434 CCTGTTGCTTTTATGCATGCAC 59.331 45.455 25.37 9.84 42.96 4.57
7914 8963 3.581755 CTGTTGCTTTTATGCATGCACT 58.418 40.909 25.37 14.70 42.96 4.40
7915 8964 3.991773 CTGTTGCTTTTATGCATGCACTT 59.008 39.130 25.37 11.24 42.96 3.16
7916 8965 3.741856 TGTTGCTTTTATGCATGCACTTG 59.258 39.130 25.37 12.57 42.96 3.16
7917 8966 3.938289 TGCTTTTATGCATGCACTTGA 57.062 38.095 25.37 8.97 38.12 3.02
7918 8967 3.577667 TGCTTTTATGCATGCACTTGAC 58.422 40.909 25.37 11.79 38.12 3.18
7919 8968 3.005578 TGCTTTTATGCATGCACTTGACA 59.994 39.130 25.37 14.37 38.12 3.58
8011 9110 6.534934 GCCGCTTTGCTAATAATGATAGTAC 58.465 40.000 0.00 0.00 0.00 2.73
8038 9137 4.508124 AGTTGAGTTTTCTAGTGTTGAGCG 59.492 41.667 0.00 0.00 0.00 5.03
8042 9141 2.870411 GTTTTCTAGTGTTGAGCGTGGT 59.130 45.455 0.00 0.00 0.00 4.16
8075 9184 5.651530 GATTCGATTGACTGACTAGGTTGA 58.348 41.667 0.00 0.00 0.00 3.18
8106 9215 3.706594 GACAGCAGGCCAGGCTATATATA 59.293 47.826 20.02 0.00 40.23 0.86
8132 9241 9.775854 ATAGTGAATGAATGAGGAAGTATCTTG 57.224 33.333 0.00 0.00 0.00 3.02
8166 9279 0.780637 ATATGCGGAGAGGAGGAGGA 59.219 55.000 0.00 0.00 0.00 3.71
8167 9280 0.111446 TATGCGGAGAGGAGGAGGAG 59.889 60.000 0.00 0.00 0.00 3.69
8168 9281 2.520741 GCGGAGAGGAGGAGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
8169 9282 3.063197 GCGGAGAGGAGGAGGAGGA 62.063 68.421 0.00 0.00 0.00 3.71
8170 9283 1.150536 CGGAGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
8171 9284 1.541672 GGAGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
8172 9285 0.996762 GGAGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
8173 9286 0.478507 GAGAGGAGGAGGAGGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69
8174 9287 0.998945 AGAGGAGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
8175 9288 2.123033 GGAGGAGGAGGAGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.432890 GGAAGGGAGGAATTGTAGAGCAG 60.433 52.174 0.00 0.00 0.00 4.24
19 20 1.422531 AGCTAGCAGATGGAAGGGAG 58.577 55.000 18.83 0.00 0.00 4.30
33 34 4.322198 CGACCTAGACCTAGACCTAGCTAG 60.322 54.167 14.20 14.20 38.05 3.42
37 38 3.555586 GCTCGACCTAGACCTAGACCTAG 60.556 56.522 5.67 9.91 35.21 3.02
38 39 2.368221 GCTCGACCTAGACCTAGACCTA 59.632 54.545 5.67 0.00 35.21 3.08
39 40 1.141455 GCTCGACCTAGACCTAGACCT 59.859 57.143 5.67 0.00 35.21 3.85
40 41 1.141455 AGCTCGACCTAGACCTAGACC 59.859 57.143 5.67 0.00 35.21 3.85
41 42 2.215196 CAGCTCGACCTAGACCTAGAC 58.785 57.143 5.67 0.00 35.21 2.59
42 43 1.475392 GCAGCTCGACCTAGACCTAGA 60.475 57.143 5.67 0.00 35.21 2.43
107 129 1.115467 ACAGAATCCCTAGCACGAGG 58.885 55.000 0.00 0.00 36.23 4.63
167 189 3.871594 GGGAATTCAGTGAATACGGTGAG 59.128 47.826 18.56 0.00 31.46 3.51
173 203 6.180472 TGAAGGAAGGGAATTCAGTGAATAC 58.820 40.000 18.56 13.94 39.91 1.89
201 231 5.746245 TGGAAGTAAAGTCAATTTTGCGTTG 59.254 36.000 0.00 0.00 32.01 4.10
376 447 3.054655 GGTCCTGGTCCTGCTTATACAAA 60.055 47.826 2.47 0.00 0.00 2.83
377 448 2.504175 GGTCCTGGTCCTGCTTATACAA 59.496 50.000 2.47 0.00 0.00 2.41
378 449 2.116238 GGTCCTGGTCCTGCTTATACA 58.884 52.381 2.47 0.00 0.00 2.29
379 450 2.103263 CTGGTCCTGGTCCTGCTTATAC 59.897 54.545 11.28 0.00 0.00 1.47
380 451 2.398588 CTGGTCCTGGTCCTGCTTATA 58.601 52.381 11.28 0.00 0.00 0.98
381 452 1.207791 CTGGTCCTGGTCCTGCTTAT 58.792 55.000 11.28 0.00 0.00 1.73
382 453 0.909610 CCTGGTCCTGGTCCTGCTTA 60.910 60.000 11.28 0.00 0.00 3.09
384 455 2.608988 CCTGGTCCTGGTCCTGCT 60.609 66.667 11.28 0.00 0.00 4.24
386 457 3.721706 GCCCTGGTCCTGGTCCTG 61.722 72.222 13.43 10.26 0.00 3.86
387 458 4.270153 TGCCCTGGTCCTGGTCCT 62.270 66.667 13.43 0.00 0.00 3.85
388 459 3.721706 CTGCCCTGGTCCTGGTCC 61.722 72.222 13.43 2.75 0.00 4.46
389 460 3.721706 CCTGCCCTGGTCCTGGTC 61.722 72.222 13.43 1.27 0.00 4.02
390 461 4.599500 ACCTGCCCTGGTCCTGGT 62.599 66.667 13.43 7.16 34.86 4.00
396 467 0.905337 GTAGACAGACCTGCCCTGGT 60.905 60.000 0.00 0.00 44.10 4.00
397 468 1.617947 GGTAGACAGACCTGCCCTGG 61.618 65.000 0.00 0.00 36.47 4.45
398 469 0.904865 TGGTAGACAGACCTGCCCTG 60.905 60.000 0.00 0.00 40.46 4.45
399 470 0.905337 GTGGTAGACAGACCTGCCCT 60.905 60.000 0.00 0.00 40.46 5.19
400 471 0.905337 AGTGGTAGACAGACCTGCCC 60.905 60.000 0.00 0.00 40.46 5.36
401 472 1.848652 TAGTGGTAGACAGACCTGCC 58.151 55.000 0.00 0.00 40.46 4.85
402 473 2.482142 GCATAGTGGTAGACAGACCTGC 60.482 54.545 0.00 0.00 40.46 4.85
403 474 3.027412 AGCATAGTGGTAGACAGACCTG 58.973 50.000 0.00 0.00 40.46 4.00
404 475 3.027412 CAGCATAGTGGTAGACAGACCT 58.973 50.000 0.00 0.00 40.46 3.85
405 476 2.482142 GCAGCATAGTGGTAGACAGACC 60.482 54.545 0.00 0.00 40.21 3.85
476 590 8.221944 TCTGGTTCAGGGTTTTATTAGAAAGAA 58.778 33.333 0.00 0.00 31.51 2.52
477 591 7.751646 TCTGGTTCAGGGTTTTATTAGAAAGA 58.248 34.615 0.00 0.00 31.51 2.52
478 592 7.362142 GCTCTGGTTCAGGGTTTTATTAGAAAG 60.362 40.741 0.00 0.00 33.88 2.62
479 593 6.433093 GCTCTGGTTCAGGGTTTTATTAGAAA 59.567 38.462 0.00 0.00 33.88 2.52
584 698 3.378742 GGAGTGTATCGCAGAAGAGAAGA 59.621 47.826 0.00 0.00 43.58 2.87
636 750 6.777526 TGAGTTTGAAAACAAAACACAAGG 57.222 33.333 8.53 0.00 41.30 3.61
699 861 2.290122 CTAGGAGGCACGCAGGACAG 62.290 65.000 0.00 0.00 0.00 3.51
700 862 2.283604 TAGGAGGCACGCAGGACA 60.284 61.111 0.00 0.00 0.00 4.02
701 863 2.496817 CTAGGAGGCACGCAGGAC 59.503 66.667 0.00 0.00 0.00 3.85
702 864 2.759973 CCTAGGAGGCACGCAGGA 60.760 66.667 1.05 0.00 0.00 3.86
703 865 2.759973 TCCTAGGAGGCACGCAGG 60.760 66.667 7.62 0.00 34.61 4.85
704 866 2.496817 GTCCTAGGAGGCACGCAG 59.503 66.667 13.15 0.00 34.61 5.18
755 926 4.020218 AGCTAGTCAGGACAGCATACAAAA 60.020 41.667 18.91 0.00 37.67 2.44
789 960 1.595093 GGCACCCTTCCAATCCAACG 61.595 60.000 0.00 0.00 0.00 4.10
902 1079 2.287547 GCCGCAATCTGAAACAGAAACA 60.288 45.455 5.57 0.00 44.04 2.83
924 1102 4.381398 CCAAAAATGCATGAACCGGTGATA 60.381 41.667 8.52 0.00 0.00 2.15
1014 1192 8.984891 TTTGAATTGGATAAGCAAGTACATTG 57.015 30.769 0.00 0.00 42.20 2.82
1032 1210 7.234355 AGTCCTCCAGTTACAAGATTTGAATT 58.766 34.615 0.00 0.00 0.00 2.17
1033 1211 6.784031 AGTCCTCCAGTTACAAGATTTGAAT 58.216 36.000 0.00 0.00 0.00 2.57
1034 1212 6.187727 AGTCCTCCAGTTACAAGATTTGAA 57.812 37.500 0.00 0.00 0.00 2.69
1035 1213 5.825593 AGTCCTCCAGTTACAAGATTTGA 57.174 39.130 0.00 0.00 0.00 2.69
1036 1214 5.875359 GGTAGTCCTCCAGTTACAAGATTTG 59.125 44.000 0.00 0.00 0.00 2.32
1037 1215 5.546499 TGGTAGTCCTCCAGTTACAAGATTT 59.454 40.000 0.00 0.00 34.23 2.17
1038 1216 5.091552 TGGTAGTCCTCCAGTTACAAGATT 58.908 41.667 0.00 0.00 34.23 2.40
1039 1217 4.684724 TGGTAGTCCTCCAGTTACAAGAT 58.315 43.478 0.00 0.00 34.23 2.40
1040 1218 4.122337 TGGTAGTCCTCCAGTTACAAGA 57.878 45.455 0.00 0.00 34.23 3.02
1041 1219 4.759782 CATGGTAGTCCTCCAGTTACAAG 58.240 47.826 0.00 0.00 38.42 3.16
1073 1251 8.438513 CAGACAGAATTGGAAAGCGTATATATG 58.561 37.037 0.00 0.00 0.00 1.78
1127 1351 6.319658 GGGAAGAAAGCATCAAGTTATCATCA 59.680 38.462 0.00 0.00 0.00 3.07
1128 1352 6.545298 AGGGAAGAAAGCATCAAGTTATCATC 59.455 38.462 0.00 0.00 0.00 2.92
1129 1353 6.430007 AGGGAAGAAAGCATCAAGTTATCAT 58.570 36.000 0.00 0.00 0.00 2.45
1152 1376 5.695851 AGTGTTAAGATTTGACTGCCAAG 57.304 39.130 0.00 0.00 35.94 3.61
1173 1397 2.028112 TCTGGAAGGTTCGATGTGGAAG 60.028 50.000 0.00 0.00 0.00 3.46
1308 1539 0.529337 CTCAGTGGATGGCGCACTAG 60.529 60.000 10.83 0.00 0.00 2.57
1323 1554 6.750148 ACAAGAGTTAAGAAGGTGTACTCAG 58.250 40.000 0.00 0.00 38.11 3.35
1824 2069 0.467290 TGGTGCCCAAGTTTGAGGAC 60.467 55.000 0.00 0.00 0.00 3.85
2236 2544 9.715121 GAAACCTATATCATACGGGATGTTAAA 57.285 33.333 0.00 0.00 36.84 1.52
2247 2555 9.220767 GAAGGTCCAATGAAACCTATATCATAC 57.779 37.037 7.54 0.00 45.21 2.39
2357 2674 6.209391 CCCAGATAGTGTCACTTCCAAAATTT 59.791 38.462 11.54 0.00 0.00 1.82
2512 2839 5.391312 AAGTTTCCAACAGCCAACATATC 57.609 39.130 0.00 0.00 0.00 1.63
2544 2873 9.162764 GCCTTTGTTTACAAGATTCTATGTCTA 57.837 33.333 5.23 0.00 37.15 2.59
2546 2875 7.750903 GTGCCTTTGTTTACAAGATTCTATGTC 59.249 37.037 5.23 0.00 37.15 3.06
2547 2876 7.230510 TGTGCCTTTGTTTACAAGATTCTATGT 59.769 33.333 0.00 6.69 37.15 2.29
2548 2877 7.538678 GTGTGCCTTTGTTTACAAGATTCTATG 59.461 37.037 0.00 0.00 37.15 2.23
2557 2889 9.817809 TTTTAATATGTGTGCCTTTGTTTACAA 57.182 25.926 0.00 0.00 0.00 2.41
2644 2976 8.320396 AGCAAGAACAGATATACTATGCAATG 57.680 34.615 0.00 0.00 33.89 2.82
2817 3150 9.816354 AAAAGAAAATAACACACTGTATGCTTT 57.184 25.926 0.00 0.00 0.00 3.51
2854 3187 3.406764 AGAACAAGCTGGATGAGAACAC 58.593 45.455 0.00 0.00 0.00 3.32
2887 3230 1.278238 GCGACGATCCTGGTGTTAAG 58.722 55.000 0.00 0.00 0.00 1.85
3180 3524 0.608640 ACTCCTTGCTTCCGTAGTGG 59.391 55.000 0.00 0.00 40.09 4.00
3288 3632 9.239002 CAGATAGGTTCTAGAATTAGTTCAACG 57.761 37.037 8.75 0.00 32.46 4.10
3431 3778 6.436218 TGAGGTTCAATAAGTACAGAGTAGCA 59.564 38.462 0.00 0.00 0.00 3.49
3664 4015 1.795170 ATTTTGCTGCAACGGTCGCT 61.795 50.000 15.72 0.00 0.00 4.93
3709 4060 8.903820 TCGTCTTCTCACATCTCTTTATGATTA 58.096 33.333 0.00 0.00 0.00 1.75
3769 4121 2.263540 CAGCTGCATGGGGTTTGC 59.736 61.111 0.00 0.00 40.55 3.68
3770 4122 1.588082 GTCAGCTGCATGGGGTTTG 59.412 57.895 9.47 0.00 0.00 2.93
3772 4124 2.360350 CGTCAGCTGCATGGGGTT 60.360 61.111 9.47 0.00 0.00 4.11
3888 4414 5.536916 ACCCTTTTATCCAAATGTCGTTTCA 59.463 36.000 0.00 0.00 0.00 2.69
4168 4713 4.841443 ATGGAAAACACGAAGGGTTTAC 57.159 40.909 0.51 0.00 37.47 2.01
4233 4778 7.587037 AAAATGTCATATATTGTGGGACAGG 57.413 36.000 8.34 0.00 41.80 4.00
4249 4794 8.154856 ACCTACTGTTAGCTTCTAAAAATGTCA 58.845 33.333 0.00 0.00 0.00 3.58
4431 5014 8.518430 TGCAGCTAATTAATTTTCAGGATGTA 57.482 30.769 5.91 0.00 37.40 2.29
4559 5142 2.826777 CTTGATGCCCTGAAGCGGGT 62.827 60.000 0.00 0.00 46.47 5.28
4568 5151 1.133976 GTATGGCTGTCTTGATGCCCT 60.134 52.381 12.47 7.48 45.56 5.19
4616 5199 7.284820 GGTATAGTTACATTTGGGCCTAAAGA 58.715 38.462 19.77 5.08 0.00 2.52
4682 5270 6.708285 ACATTTAGTAGGAAGATGGTTCGTT 58.292 36.000 0.00 0.00 0.00 3.85
4755 5343 4.063529 CCATGCAGAACACGTGGT 57.936 55.556 21.57 14.94 39.04 4.16
4785 5374 8.679100 CACGTGGAAATAATAGGTCCAAAAATA 58.321 33.333 7.95 0.00 42.97 1.40
4872 5501 7.958053 AAGAATTTGAAAGCCTCAAGAAATG 57.042 32.000 0.00 0.00 44.84 2.32
5077 5713 3.290710 ACATGAACCCACAGGATATTGC 58.709 45.455 0.00 0.00 36.73 3.56
5167 5803 2.052782 AACCCAACTGACCTTGACAC 57.947 50.000 0.00 0.00 0.00 3.67
5267 5903 5.163416 TGTCTGATGATCGCTTCAAGGAATA 60.163 40.000 0.00 0.00 38.03 1.75
5278 5914 4.510711 AGATGTTGAATGTCTGATGATCGC 59.489 41.667 0.00 0.00 0.00 4.58
5512 6149 3.438781 GCTCGTATGATCCCAGACTAGAG 59.561 52.174 0.00 0.00 31.38 2.43
5519 6156 2.477825 CAGTTGCTCGTATGATCCCAG 58.522 52.381 0.00 0.00 0.00 4.45
6018 6655 3.187227 CGCAGCAAGACAGAACTTGTTAT 59.813 43.478 0.00 0.00 45.98 1.89
6351 6991 8.850156 GCAGTATGTTCCCTTATCAAATGTTAT 58.150 33.333 0.00 0.00 39.31 1.89
6410 7050 7.383029 CGTATCTGACAGGTTACAAGTTAAACA 59.617 37.037 1.81 0.00 0.00 2.83
6411 7051 7.620806 GCGTATCTGACAGGTTACAAGTTAAAC 60.621 40.741 1.81 0.00 0.00 2.01
6412 7052 6.366877 GCGTATCTGACAGGTTACAAGTTAAA 59.633 38.462 1.81 0.00 0.00 1.52
6460 7110 7.787028 TCCACAAGGCTACTTAAATTTTTGTT 58.213 30.769 0.00 0.00 34.49 2.83
6528 7178 9.929180 GTAGCTAAGTGGATCATGAATACATTA 57.071 33.333 0.00 0.00 34.15 1.90
6910 7609 2.906389 TGACAAGAGGCTCCATGTTAGT 59.094 45.455 20.46 6.42 0.00 2.24
7016 7715 5.558818 AGAGATGCTGGATAATCATTCACC 58.441 41.667 0.00 0.00 0.00 4.02
7025 7724 1.335964 GCGCGTAGAGATGCTGGATAA 60.336 52.381 8.43 0.00 35.24 1.75
7066 7765 5.352293 TCAACACACATGCTCAACTATCATC 59.648 40.000 0.00 0.00 0.00 2.92
7067 7766 5.247862 TCAACACACATGCTCAACTATCAT 58.752 37.500 0.00 0.00 0.00 2.45
7068 7767 4.640364 TCAACACACATGCTCAACTATCA 58.360 39.130 0.00 0.00 0.00 2.15
7090 7789 5.244626 AGAACAAAGTTATCCTGCAGCAAAT 59.755 36.000 8.66 3.95 0.00 2.32
7400 8103 8.062448 GCTGTTCAACCGACATTAATATAAGTC 58.938 37.037 0.00 0.00 0.00 3.01
7443 8146 7.830099 TCCTACCTAATAAGTAGTTGCCTAC 57.170 40.000 0.00 0.00 43.32 3.18
7447 8150 9.833917 ATTTCTTCCTACCTAATAAGTAGTTGC 57.166 33.333 0.00 0.00 36.30 4.17
7598 8428 0.031178 CAAGCACAACAGTTGCTCCC 59.969 55.000 13.56 0.00 38.01 4.30
7599 8429 0.031178 CCAAGCACAACAGTTGCTCC 59.969 55.000 13.56 2.01 38.01 4.70
7609 8439 4.365514 TCCTAATGAGAACCAAGCACAA 57.634 40.909 0.00 0.00 0.00 3.33
7755 8586 4.216902 GCAAAATACGGTACCCAGTTCTTT 59.783 41.667 6.25 1.12 0.00 2.52
7756 8587 3.754850 GCAAAATACGGTACCCAGTTCTT 59.245 43.478 6.25 0.00 0.00 2.52
7757 8588 3.244630 TGCAAAATACGGTACCCAGTTCT 60.245 43.478 6.25 0.00 0.00 3.01
7758 8589 3.075884 TGCAAAATACGGTACCCAGTTC 58.924 45.455 6.25 0.00 0.00 3.01
7851 8900 5.066505 CACTTTCCAGCAAACAGAAACTACT 59.933 40.000 0.00 0.00 0.00 2.57
7861 8910 2.287849 GGCTTCTCACTTTCCAGCAAAC 60.288 50.000 0.00 0.00 31.71 2.93
7909 8958 4.661222 TCAGGGATTAATTGTCAAGTGCA 58.339 39.130 0.00 0.00 0.00 4.57
7910 8959 5.841957 ATCAGGGATTAATTGTCAAGTGC 57.158 39.130 0.00 0.00 0.00 4.40
7911 8960 6.263168 GGGTATCAGGGATTAATTGTCAAGTG 59.737 42.308 0.00 0.00 0.00 3.16
7912 8961 6.365520 GGGTATCAGGGATTAATTGTCAAGT 58.634 40.000 0.00 0.00 0.00 3.16
7913 8962 5.470098 CGGGTATCAGGGATTAATTGTCAAG 59.530 44.000 0.00 0.00 0.00 3.02
7914 8963 5.104277 ACGGGTATCAGGGATTAATTGTCAA 60.104 40.000 0.00 0.00 0.00 3.18
7915 8964 4.410883 ACGGGTATCAGGGATTAATTGTCA 59.589 41.667 0.00 0.00 0.00 3.58
7916 8965 4.755123 CACGGGTATCAGGGATTAATTGTC 59.245 45.833 0.00 0.00 0.00 3.18
7917 8966 4.445735 CCACGGGTATCAGGGATTAATTGT 60.446 45.833 0.00 0.00 0.00 2.71
7918 8967 4.072131 CCACGGGTATCAGGGATTAATTG 58.928 47.826 0.00 0.00 0.00 2.32
7919 8968 3.073946 CCCACGGGTATCAGGGATTAATT 59.926 47.826 0.00 0.00 44.30 1.40
7954 9003 6.839124 ATACTTGAAAGAAACATCATGCCA 57.161 33.333 0.00 0.00 0.00 4.92
7981 9080 5.411361 TCATTATTAGCAAAGCGGCGAATAT 59.589 36.000 12.98 0.00 39.80 1.28
7984 9083 2.939756 TCATTATTAGCAAAGCGGCGAA 59.060 40.909 12.98 0.00 39.27 4.70
8011 9110 7.218963 GCTCAACACTAGAAAACTCAACTTTTG 59.781 37.037 0.00 0.00 0.00 2.44
8016 9115 4.270325 ACGCTCAACACTAGAAAACTCAAC 59.730 41.667 0.00 0.00 0.00 3.18
8038 9137 6.308282 GTCAATCGAATCGAATAGGATACCAC 59.692 42.308 10.12 0.00 39.99 4.16
8042 9141 7.175119 AGTCAGTCAATCGAATCGAATAGGATA 59.825 37.037 10.12 0.00 39.99 2.59
8075 9184 0.746659 GGCCTGCTGTCAACAAAAGT 59.253 50.000 0.00 0.00 0.00 2.66
8106 9215 9.775854 CAAGATACTTCCTCATTCATTCACTAT 57.224 33.333 0.00 0.00 0.00 2.12
8132 9241 2.469147 CGCATATCGACATGACTGACAC 59.531 50.000 8.12 0.00 41.67 3.67


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.